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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model Implementation
894EBPJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
 2009-02-12 00:00:00		General Mammalian /
E.coli Expression		Surface, CytosolQuantitative match to experiments, Qualitative /
Exact GENESIS implementation
71RasGTPasePhillips RA et al Biochemistry. 2003 Apr 8;42(13):3956-65. ( Peer-reviewed publication ) /
 2006-05-12 00:00:00		General Mammalian /
E.coli Expression system		CytosolQualitative /
Exact GENESIS implementation
69
  • Quorum_
    repressilator
    		•  Garcia-Ojalvo J, Elowitz MB, Strogatz SH. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10955-60.. ( Peer-reviewed publication ) /
     2006-02-14 00:00:00    		E. Coli /
    E.coli Expression, Transposon Tn10, Lambda phage Expression    		Cytosol, ExtracellularQualitative /
    Exact GENESIS implementation
    68RepressilatorElowitz MB, Leibler S., Nature. 2000 Jan 20;403(6767):335-8. ( Peer-reviewed publication ) /
     2006-02-13 00:00:00    		E. Coli /
    E.coli Expression, Transposon, Lambda phage    		CytosolQualitative /
    Exact GENESIS implementation
    43
  • CDK2-CyclinA_
    activation_
    improved
    		• Morris MC. et al. J Biol Chem. (2002) 277(26):23847-53. ( peer-reviewed publication ) /
     2003-01-11 00:00:00    		Human, Xenopus /
    Expressed in E.coli    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    42
  • CDK2-CyclinA_
    activation_
    pathway
    		• Morris MC. et al. J Biol Chem. (2002) 277(26):23847-53. ( peer-reviewed publication ) /
     2003-01-11 00:00:00    		Human, Xenopus /
    Expressed in E.coli    		CytosolQualitative /
    Exact GENESIS implementation
    47PKA_2003Bhalla US. (2004) Biophys J. 87(2):733-44. ( peer-reviewed publication ) /
     2003-04-28 00:00:00    		Generic mammalian /
    Generic    		Cytosol + Cell membraneQualitative /
    Exact GENESIS implementation
    48PKC_2003Bhalla US. (2004) Biophys J. 87(2):733-44 .( peer-reviewed publication ) /
     2003-04-28 00:00:00    		Generic mammalian /
    Generic    		Cytosol + Cell membraneQualitative /
    Exact GENESIS implementation
    88S6KJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    HEK293 cells    		Surface, CytosolQualitative /
    Exact GENESIS implementation
    70RanGTPaseGorlich D et al EMBO J. 2003 Mar 3;22(5):1088-100. ( Peer-reviewed publication ) /
     2006-05-12 00:00:00    		Eukaryotic system /
    HeLa Cells    		Cytosol, NucleusQualitative /
    Exact GENESIS implementation
    52
  • EGFR_Signaling_
    pathway
    		• Quantification of Short Term Signaling by the EGFR Kholodenko et al, The J Biol Chem. , Vol 274, No. 42, Issue of October 15, pp. 30169 - 30181, 1999. ( peer-reviewed publication ) /
     2003-05-17 00:00:00    		Harlan Sprague Dawley rat; mammalian /
    Hepatocytes    		Cell membrane + cytosolQualitative /
    Mathematically equivalent
    80
  • Ajay_Bhalla_
    2007_PKM
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    79
  • Ajay_Bhalla_
    2007_Bistable
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    78
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning
    		• Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) /
     2006-12-12 00:00:00    		Rat /
    Hippocampal CA1    		DendritesSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    81
  • Ajay_bhalla_
    2007_ReacDiff1_
    1e-12
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    77
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning
    		• Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80 ( Peer-reviewed publication ) /
     2006-12-12 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    76
  • Ajay_Bhalla_
    2004_PKM_Tuning
    		• Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) /
     2006-12-12 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi -Quantitative match to experiments /
    Exact GENESIS implementation
    82
  • Ajay_Bhalla_
    2007_ReacDiff1_
    1e-13
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    83
  • Ajay_Bhalla_
    2007_ReacDiff2
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    84
  • Ajay_Bhalla_
    2007_ReacDiff3
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    74NMArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    73HomoArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    72L-ArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		Human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    75NOHArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    66
  • Jak-Stat_
    Pathway
    		• Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6. ( Peer-reviewed publication ) /
     2006-02-13 00:00:00    		mouse /
    Liver    		Cytosol, NucleusQuantitative match to experiments /
    Exact GENESIS implementation
    67SOCS1_knockoutYamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6. ( Peer-reviewed publication ) /
     2006-02-13 00:00:00    		mouse /
    Liver    		Nucleus , cytoplasmQuantitative match to experiments /
    Exact GENESIS implementation
    15
  • sGC_Stone_
    Marletta
    		• Stone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9. ( peer-reviewed publication ) /
     2001-12-12 00:00:00    		Bovine /
    Lungs    		CytosolQuantitative match to experiments /
    Mathematically equivalent
    28
  • CO_activation_
    of_GC
    		• In-house  /
     2002-01-22 00:00:00    		Bovine /
    Lungs    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    65
  • AMPAR_CaMKII_
    weak_coupling
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-21 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    2fig3_CaMKIIBhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-11-07 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    3fig4_synapseBhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-11-07 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQuantitative match to experiments, Qualitative, Hypothetical /
    Exact GENESIS implementation
    16
  • Synaptic_
    Network
    		• Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-12-12 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    18Kuroda_GCKuroda S. et al. J Neurosci. (2001) 21(15):5693-702. ( peer-reviewed publication ) /
     2001-12-24 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQuantitative match to experiments /
    Exact GENESIS implementation
    96BCMBhalla PLoS Comput Biol 2021 (peer reviewed publication) /
     2022-05-19 00:00:00    		General Mammalian /
    Neuronal    		Cell membrane/cytosolQualitative /
    Reduced ODE model
    95
  • Differential syn
    thesis of mRNA
    		• Peer-reviewed publication,Book /
     2014-06-10 00:00:00    		General Mammalian/Neuronal /
    Neuronal    		Surface,Cytosol, NucleusQuantitative match to experiments,Approximate implementation,Qualitative,Qualitative /
    Approximate implementation
    94mRNA synthesisPeer-reviewed publication,Book /
     2014-06-10 00:00:00    		General Mammalian/Neuronal /
    Neuronal    		Surface,Cytosol, NucleusQuantitative match to experiments,Approximate implementation,Qualitative,Qualitative /
    Approximate implementation
    61
  • simple_AMPAR_
    traff_model2
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Postsynaptic Density, Synaptic SpineIllustrative /
    Exact GENESIS implementation
    64
  • AMPAR_CaMKII_
    strong_coupling
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    63CaMKII_model3Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    62
  • CaMKII_noPKA_
    model3
    		• Hayer A, Bhalla US PLoS PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation